Contacts of the helix formed by residues 156 - 168 (chain D) in PDB entry 2FMM
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 156 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D PHE* 3.9 23.6 - - - -
119D PRO* 3.7 29.2 - - + -
122D ILE* 6.0 0.2 - - - -
136D MET* 5.1 2.9 - - - -
152D ALA* 2.9 24.7 + - - -
155D LYS* 1.3 80.3 - - + +
157D PRO* 1.3 65.7 - - - +
159D VAL* 3.0 24.5 + - + -
160D VAL* 3.2 9.0 + - - +
602D SO4 3.2 21.1 - - - +
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Residues in contact with PRO 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C PRO* 4.0 19.7 - - + -
158C GLN* 4.0 13.0 - - - +
161C ILE* 3.9 3.5 - - + +
152D ALA 4.3 0.9 - - - +
153D ASN 3.3 19.7 - - - +
154D VAL 3.4 17.0 - - - +
155D LYS 3.6 1.8 - - - +
156D CYS* 1.3 88.5 - - - +
158D GLN* 1.3 61.3 + - + +
160D VAL* 3.3 6.6 + - + +
161D ILE* 2.9 34.8 + - + +
602D SO4 3.3 14.6 - - - +
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Residues in contact with GLN 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ASN* 2.9 42.4 + - - +
154C VAL* 4.5 9.6 + - - +
157C PRO* 4.1 9.9 - - - +
157D PRO* 1.3 76.6 - - + +
159D VAL* 1.3 60.7 + - - +
161D ILE* 3.8 13.6 - - - +
162D SER* 2.8 35.8 + - - +
602D SO4 3.1 27.8 + - - +
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Residues in contact with VAL 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D PRO* 4.4 17.9 - - + +
120D GLU 4.5 6.5 - - - +
121D ARG* 4.0 20.4 - - - -
122D ILE* 3.9 22.4 + - + -
136D MET* 4.2 10.1 - - - -
156D CYS* 3.0 20.6 + - + +
158D GLN* 1.3 76.5 - - - +
160D VAL* 1.3 61.8 + - - +
162D SER* 3.6 6.5 + - - -
163D PHE* 3.1 22.5 + - - +
602D SO4 3.0 21.2 + - - +
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Residues in contact with VAL 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ILE* 3.2 21.3 - - + -
122D ILE* 3.9 9.9 - - + -
134D PHE* 3.9 14.4 - - + -
152D ALA* 3.6 35.9 - - + +
153D ASN* 3.6 16.4 - - - +
156D CYS* 3.2 14.3 + - - +
157D PRO* 3.6 7.0 - - + +
158D GLN 3.2 0.2 - - - -
159D VAL* 1.3 75.3 - - - +
161D ILE* 1.3 64.8 + - - +
163D PHE* 3.2 5.1 + - + +
164D TYR* 3.1 40.2 + - + -
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Residues in contact with ILE 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ASN* 3.4 59.2 - - + +
157C PRO* 3.9 21.8 - - + +
160C VAL* 4.2 11.9 - - + -
161C ILE* 3.1 19.3 - - + -
164C TYR* 4.6 3.8 - - + -
157D PRO 2.9 20.9 + - - +
158D GLN* 3.8 18.8 - - - +
160D VAL* 1.3 76.3 - - - +
162D SER* 1.3 57.6 + - - +
164D TYR* 3.3 5.1 + - - +
165D GLU* 2.9 35.3 + - - +
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Residues in contact with SER 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D GLN* 2.8 23.9 + - - +
159D VAL* 3.7 7.5 - - - -
161D ILE* 1.3 77.0 - - - +
163D PHE* 1.3 63.7 + - - +
165D GLU* 3.5 5.6 + - - +
166D GLU* 3.0 38.7 + - - +
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Residues in contact with PHE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C LEU* 6.0 0.2 - - + -
122D ILE* 3.4 50.9 - - + +
124D GLY* 4.0 11.4 - - - -
125D ALA* 3.8 31.0 - - + -
134D PHE* 3.9 13.9 - + - -
159D VAL 3.1 11.8 + - - +
160D VAL 3.2 9.2 + - - +
162D SER* 1.3 81.0 - - - +
164D TYR* 1.3 85.2 + + - +
166D GLU* 4.5 2.5 - - - -
167D ARG* 3.0 72.3 + - - +
99E LEU 4.6 9.0 - - - -
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Residues in contact with TYR 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C ILE* 4.1 18.2 - - + -
164C TYR* 3.4 43.7 - + + -
165C GLU* 3.8 9.9 + - - +
168C LEU* 3.6 34.5 - - + +
132D LEU* 3.4 18.5 - - - +
134D PHE* 3.2 23.5 - + - -
153D ASN* 5.2 0.2 + - - -
160D VAL* 3.1 34.0 + - + +
161D ILE 3.8 2.5 - - - +
163D PHE* 1.3 99.7 - + - +
165D GLU* 1.3 66.3 + - - +
167D ARG* 3.0 4.9 + - - -
168D LEU* 3.0 22.7 + - - +
99E LEU 6.0 0.2 - - - -
101E PRO* 3.9 11.8 - - + +
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Residues in contact with GLU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C LEU* 3.7 24.8 - - + +
149C ALA* 4.8 3.3 - - - +
153C ASN* 3.0 30.6 + - - +
164C TYR* 3.6 22.4 + - + +
161D ILE* 2.9 25.4 + - - +
162D SER* 4.0 4.8 - - - +
164D TYR* 1.3 73.7 - - - +
166D GLU* 1.3 63.2 + - + +
167D ARG 3.3 0.5 + - - -
168D LEU* 3.5 15.5 + - - +
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Residues in contact with GLU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D SER* 3.0 30.0 + - - +
163D PHE* 4.5 1.4 - - - -
164D TYR 3.2 0.2 - - - -
165D GLU* 1.3 77.6 - - + +
167D ARG* 1.3 84.7 + - - +
168D LEU 3.5 1.3 - - - +
98E ARG* 5.4 1.4 + - - -
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Residues in contact with ARG 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ARG* 5.0 8.1 - - - +
122D ILE 3.8 16.0 + - - -
123D ILE* 4.4 10.5 + - - +
124D GLY* 5.8 0.2 - - - -
163D PHE* 3.0 59.0 + - - +
164D TYR* 3.0 5.8 + - - +
166D GLU* 1.3 104.7 + - - +
168D LEU* 1.3 68.6 + - - +
169D THR* 2.9 16.2 + - - -
68E ARG* 5.9 3.6 - - - +
98E ARG* 3.5 37.7 + - - +
99E LEU 4.5 6.1 - - - -
100E VAL* 3.5 21.5 - - + +
101E PRO* 4.0 7.9 - - + -
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Residues in contact with LEU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C ALA* 5.1 2.2 - - + -
132C LEU* 3.8 39.5 - - + -
164C TYR* 4.1 12.8 - - + -
164D TYR 3.0 10.7 + - - +
165D GLU* 3.5 15.1 + - - +
166D GLU 3.5 1.6 - - - +
167D ARG* 1.3 75.8 - - - +
169D THR* 1.3 64.2 + - - +
170D TRP* 3.9 27.1 + - + +
101E PRO* 3.7 12.3 - - + +
103E MET* 3.3 44.4 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il